Ziziphus lotus is an underappreciated natural genetic resource widespread in Algeria. This study aimed to compare the fruit phytochemical composition of nine populations of Z. lotus from different areas to highlight its diversity. Fruits were harvested from the semiarid, dry steppe and Saharan stages. Primary and secondary metabolites and minerals contents were determined. Significant variations in the fruit phytochemical composition between populations of Z. lotus and between pulp and seeds were recorded. Z. lotus is dry fruit with 8.768 ± 0.449 to 13.468 ± 1.303% water in pulp and 6.7 to 12.12% in seeds. Significantly higher values were recorded in the fruit pulp for sugar (35.25 to 48.87%), phosphorus (63.114 to 155.269 mg 100−1g), sodium (34.8 to 56.91 ppm), calcium (91.78 to 382.69 ppm), β-carotene (36.4 to 46 μg g−1), lycopene (59.15 to 100.25 μg g−1) and chlorophyll a (3.6 to 7.2 μg g−1) contents. Seeds had much higher protein (8.37 to 27.75%), lipid (35.39 to 48.01%), potassium (125.874 to 325.408 mg. 100−1 g), polyphenol (439.465 to 1349.46 mg.GAE.100 g−1), flavonoid (83.908 to 98.259 mg.QE.100 g−1), tannins (55.268 to 277.94 mg.GAE.100 g−1) and chlorophyll b (11.2 to 30.4 μg g−1) contents. Bougtob, Boghar and Mougheul populations had higher primary metabolites and mineral values. Oued Nougued, Maarif and Mougheul populations were the richest in phenolic compounds. Oued Nougued, Maarif and Mougheul populations had more liposoluble pigments. This research is the beginning of investigating the variety of Z. lotus as phylogenetic sources. Further comparative investigations over a larger distribution region and further study of variations in the composition in fruit composition using GC-MS are needed.